A Guatemalan court indicted former president Otto Perez on corruption charges, days after he resigned over a customs fraud scandal that stoked outrage in the Central American country.

Judge Miguel Angel Galvez granted prosecutors' request to try Perez on charges of customs fraud, racketeering and bribery, and ruled the fallen conservative leader must remain in custody.

The judge on Tuesday also gave the prosecution three months to continue its investigation, after which the 64-year-old retired general will face trial.

"I don't understand why I've been charged," a distraught Perez told journalists as police escorted him from the court.

"There's not a single piece of evidence," he said. "I'm sure I have never participated in any criminal network."

His next court date was set for Dec 21.

Prosecutors and investigators from a UN commission tasked with fighting high-level graft in Guatemala accused Perez of orchestrating a scheme in which businesses bribed corrupt officials to clear their imports through customs at a fraction of the actual tax rate.

They said the accusations are based on some 89,000 wiretapped phone calls.

The scheme - dubbed La Linea, for a hotline businesses reportedly called to access a network of corrupt officials - collected $3.8 million in bribes between May 2014 and April this year, including $800,000 each to Perez and jailed former vice-president Roxana Baldetti, prosecutors said.

Perez, who denied the charges, defied months of mass protests calling on him to quit, but was left with little choice after Congress stripped him of his immunity and a judge issued a warrant for his arrest last week.

He resigned on Sept 2.

The country, meanwhile, held general elections on Sunday in a climate of widespread mistrust of politics.

Comedian and political novice Jimmy Morales won the presidential race.

Newly sworn-in President Alejandro Maldonado, a former Constitutional Court judge, will serve the remainder of Perez's term, which ends on Jan 14.

AFP - Reuters